Differences

This shows you the differences between two versions of the page.

--- abyss-software [2014/06/10 21:47] – created aorth
+++ abyss-software [2019/07/10 14:25] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== Abyss ======
-Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
+Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
 ===== Information =====
-  * Version: 1.5.1
+  * Version: 2.1.4
   * Added: August, 2013
-  * Updated: June 10, 2014
+  * Updated: November, 2018
+  * K-mer size: 128 (default at compile time)
   * Link: http://www.bcgsc.ca/platform/bioinfo/software/abyss
 ===== Usage =====
-=== See versions of abyss which are available ===
+See versions of abyss which are available:
-<code>module avail abyss</code>
+<code>$ module avail abyss</code>
+Load one version into your environment and run it:
+<code>$ module load abyss/2.1.4
+$ abyss-pe help</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>wget https://github.com/bcgsc/abyss/releases/download/1.5.1/abyss-1.5.1.tar.gz
+<code>$ cd /tmp
-tar zxf abyss-1.5.1.tar.gz
+$ wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.4/abyss-2.1.4.tar.gz
-cd abyss-1.5.1
+$ tar xf abyss-2.1.4.tar.gz
-scl enable devtoolset-1.1 bash
+$ cd abyss-2.1.4
-mkdir /tmp/abyss-build
+$ sudo yum install sparsehash-devel.x86_64 openmpi3-devel.x86_64
-cd /tmp/abyss-build
+$ export CPPFLAGS='-pthread -I/usr/include/openmpi3-x86_64'
-~/src/abyss-1.5.1/configure --prefix=/export/apps/abyss/1.5.1 --with-boost=/export/apps/boost/1.50.0/include/
+$ export LIBS='-Wl,-rpath -Wl,/usr/lib64/openmpi3/lib -Wl,--enable-new-dtags -L/usr/lib64/openmpi3/lib -lmpi'
-sudo mkdir -p /export/apps/abyss/1.5.1
+$ ./configure --prefix=/export/apps/abyss/2.1.4
-sudo chown aorth /export/apps/abyss/1.5.1
+$ make -j4
-sudo chown -R root:root /export/apps/abyss/1.5.1</code>
+$ sudo mkdir -p /export/apps/abyss/2.1.4
+$ sudo chown aorth /export/apps/abyss/2.1.4
+$ make install
+$ sudo chown -R root:root /export/apps/abyss/2.1.4
+$ sudo yum remove sparsehash-devel.x86_64 openmpi3-devel.x86_64</code>
+There is currently a [[https://github.com/bcgsc/abyss/issues/224|bug in configure's ability to detect the system's OpenMPI]] so we have to set the environment variables manually before building.